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ReactionMechanismGenerator / RMG-Java

The Java version of RMG: Reaction Mechanism Generator
http://rmg.sourceforge.net/
MIT License
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ClassNotFoundException: jing.chem.molFile #133

Closed rwest closed 12 years ago

rwest commented 13 years ago

This is a job with QMTP and many pre-existing saved QM files. The job runs for a while, happily reading in the existing files, until the model core has 2059 reactions and 81 species and the model edge has 5900 reactions and 4091 species, then suddenly it can't find the jing/chem/molFile class. 

Created new reaction: CO3(4171) + CH2OJJ(111) --> C2H2O4JJ(4237)
Pre-existing successful quantum result for HLXXQRFZDITDHQ-UHFFFAOYAE (InChI=1/C2H4O4/c1-3-4-2-5-6-2/h2H,1H3) has been found. This log file will be used.
Point group: Cs
Thermo for HLXXQRFZDITDHQ-UHFFFAOYAE: -31.57    84.61   23.93   28.58   32.63   35.94   40.84   44.24   49.18   
HBI-based thermo for GRSHUWISPXYGAZ-UHFFFAOYAEmult3(InChI=1/C2H2O4/c1-3-4-2-5-6-2/h1H2/mult3): 63.67    85.6    22.85   26.74   29.9    32.32   35.69   37.88   40.89   
Created new species: C2H2O4JJ(4238)
Ea raised by 48.0 from 5.0 to dHrxn(298K)=53.0 kcal/mol.
Created new reaction: CO3(4171) + CH2OJJ(111) --> C2H2O4JJ(4238)
Created new reaction: CO3(4171) + CH2OJJ(111) --> C2H2O4JJ(2182)
Exception in thread "main" java.lang.NoClassDefFoundError: jing/chem/molFile
    at jing.chem.QMTP.create3Dmolfile(QMTP.java:401)
    at jing.chem.QMTP.generateQMThermoData(QMTP.java:256)
    at jing.chem.QMTP.generateThermoData(QMTP.java:148)
    at jing.chem.ChemGraph.generateThermoData(ChemGraph.java:1300)
    at jing.chem.ChemGraph.getThermoData(ChemGraph.java:1821)
    at jing.chem.Species.findStablestThermoData(Species.java:338)
    at jing.chem.Species.(Species.java:118)
    at jing.chem.Species.make(Species.java:872)
    at jing.rxn.ReactionTemplate.reactTwoReactants(ReactionTemplate.java:1196)
    at jing.rxn.TemplateReactionGenerator.react(TemplateReactionGenerator.java:191)
    at jing.rxnSys.RateBasedPDepRME.addSpeciesToCore(RateBasedPDepRME.java:318)
    at jing.rxnSys.RateBasedPDepRME.enlargeReactionModel(RateBasedPDepRME.java:235)
    at jing.rxnSys.ReactionModelGenerator.enlargeReactionModel(ReactionModelGenerator.java:3977)
    at jing.rxnSys.ReactionModelGenerator.modelGeneration(ReactionModelGenerator.java:1452)
    at RMG.main(RMG.java:57)
Caused by: java.lang.ClassNotFoundException: jing.chem.molFile
    at java.net.URLClassLoader$1.run(URLClassLoader.java:214)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.net.URLClassLoader.findClass(URLClassLoader.java:205)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:321)
    at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:266)
    ... 15 more
Caused by: java.util.zip.ZipException: error reading zip file
    at java.util.zip.ZipFile.read(Native Method)
    at java.util.zip.ZipFile.access$1200(ZipFile.java:46)
    at java.util.zip.ZipFile$ZipFileInputStream.read(ZipFile.java:464)
    at java.util.zip.ZipFile$1.fill(ZipFile.java:247)
    at java.util.zip.InflaterInputStream.read(InflaterInputStream.java:158)
    at java.util.jar.Manifest$FastInputStream.fill(Manifest.java:439)
    at java.util.jar.Manifest$FastInputStream.readLine(Manifest.java:375)
    at java.util.jar.Manifest$FastInputStream.readLine(Manifest.java:407)
    at java.util.jar.Attributes.read(Attributes.java:376)
    at java.util.jar.Manifest.read(Manifest.java:199)
    at java.util.jar.Manifest.(Manifest.java:69)
    at java.util.jar.JarFile.getManifestFromReference(JarFile.java:182)
    at java.util.jar.JarFile.getManifest(JarFile.java:163)
    at sun.misc.URLClassPath$JarLoader$2.getManifest(URLClassPath.java:710)
    at java.net.URLClassLoader.defineClass(URLClassLoader.java:238)
    at java.net.URLClassLoader.access$000(URLClassLoader.java:73)
    at java.net.URLClassLoader$1.run(URLClassLoader.java:212)
    ... 20 more

This java code was compiled by ant at:
2011-01-25T20:34:57 The git repository was on the branch:
master And at the commit with the hash:
139bb8fc360862169290100c6a0bcc0788de1b4e To see changes since then visit: http://github.com/GreenGroup/RMG-Java/compare/139bb8...master

rwest commented 13 years ago

I moved the folder of 5000 quantum calculation files to one side and started the job again. It has progressed beyond the point at which it failed last time, so I am closing this bug as "cannot reproduce".

rwest commented 13 years ago

Reopened. This just happened again, on the same job. (but with new qm files)


Ea raised by 4.1 from 11.9 to dHrxn(298K)=16.0 kcal/mol.
Created new reaction: C2H3O3J(216) + CH3O2J(677) --> C3H6O5JJ(6938)
Created new species: C3H6O5JJ(6939)
Ea raised by 15.3 from 5.0 to dHrxn(298K)=20.3 kcal/mol.
Created new reaction: C2H3O3J(216) + CH3O2J(677) --> C3H6O5JJ(6939)
Exception in thread "main" java.lang.NoClassDefFoundError: jing/chem/molFile
    at jing.chem.QMTP.create3Dmolfile(QMTP.java:401)
    at jing.chem.QMTP.generateQMThermoData(QMTP.java:256)
    at jing.chem.QMTP.generateThermoData(QMTP.java:148)
    at jing.chem.ChemGraph.generateThermoData(ChemGraph.java:1300)
    at jing.chem.ChemGraph.getThermoData(ChemGraph.java:1821)
    at jing.chem.Species.findStablestThermoData(Species.java:338)
    at jing.chem.Species.(Species.java:118)
    at jing.chem.Species.make(Species.java:878)
    at jing.rxn.ReactionTemplate.reactTwoReactants(ReactionTemplate.java:1196)
    at jing.rxn.TemplateReactionGenerator.react(TemplateReactionGenerator.java:194)
    at jing.rxnSys.RateBasedPDepRME.addSpeciesToCore(RateBasedPDepRME.java:317)
    at jing.rxnSys.RateBasedPDepRME.enlargeReactionModel(RateBasedPDepRME.java:235)
    at jing.rxnSys.ReactionModelGenerator.enlargeReactionModel(ReactionModelGenerator.java:3977)
    at jing.rxnSys.ReactionModelGenerator.modelGeneration(ReactionModelGenerator.java:1452)
    at RMG.main(RMG.java:57)
Caused by: java.lang.ClassNotFoundException: jing.chem.molFile
    at java.net.URLClassLoader$1.run(URLClassLoader.java:214)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.net.URLClassLoader.findClass(URLClassLoader.java:205)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:321)
    at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:266)
    ... 15 more
Caused by: java.util.zip.ZipException: error reading zip file
    at java.util.zip.ZipFile.read(Native Method)
    at java.util.zip.ZipFile.access$1200(ZipFile.java:46)
    at java.util.zip.ZipFile$ZipFileInputStream.read(ZipFile.java:464)
    at java.util.zip.ZipFile$1.fill(ZipFile.java:247)
    at java.util.zip.InflaterInputStream.read(InflaterInputStream.java:158)
    at java.util.jar.Manifest$FastInputStream.fill(Manifest.java:439)
    at java.util.jar.Manifest$FastInputStream.readLine(Manifest.java:375)
    at java.util.jar.Manifest$FastInputStream.readLine(Manifest.java:407)
    at java.util.jar.Attributes.read(Attributes.java:376)
    at java.util.jar.Manifest.read(Manifest.java:199)
    at java.util.jar.Manifest.(Manifest.java:69)
    at java.util.jar.JarFile.getManifestFromReference(JarFile.java:182)
    at java.util.jar.JarFile.getManifest(JarFile.java:163)
    at sun.misc.URLClassPath$JarLoader$2.getManifest(URLClassPath.java:710)
    at java.net.URLClassLoader.defineClass(URLClassLoader.java:238)
    at java.net.URLClassLoader.access$000(URLClassLoader.java:73)
    at java.net.URLClassLoader$1.run(URLClassLoader.java:212)
    ... 20 more

This java code was compiled by ant at:
2011-01-26T00:09:42 The git repository was on the branch:
master And at the commit with the hash:
5ad0fa99f926ef962a274a6d74b35a5c31e41af6 To see changes since then visit: http://github.com/GreenGroup/RMG-Java/compare/5ad0fa...master

rwest commented 13 years ago

This just happened again.


Created new species: C4H6O5(5864)
Created new 2+2_cycloaddition_CO reaction: C2H2O4(1170) + CH3CHO(15) --> C4H6O5(5864)
Exception in thread "main" java.lang.NoClassDefFoundError: jing/chem/molFile
    at jing.chem.QMTP.create3Dmolfile(QMTP.java:402)
    at jing.chem.QMTP.generateQMThermoData(QMTP.java:257)
    at jing.chem.QMTP.generateThermoData(QMTP.java:223)
    at jing.chem.ChemGraph.generateThermoData(ChemGraph.java:1304)
    at jing.chem.ChemGraph.getThermoData(ChemGraph.java:1812)
    at jing.chem.Species.findStablestThermoData(Species.java:337)
    at jing.chem.Species.(Species.java:117)
    at jing.chem.Species.make(Species.java:877)
    at jing.rxn.ReactionTemplate.reactTwoReactants(ReactionTemplate.java:1197)
    at jing.rxn.TemplateReactionGenerator.react(TemplateReactionGenerator.java:165)
    at jing.rxnSys.RateBasedPDepRME.addSpeciesToCore(RateBasedPDepRME.java:313)
    at jing.rxnSys.RateBasedPDepRME.enlargeReactionModel(RateBasedPDepRME.java:233)
    at jing.rxnSys.ReactionModelGenerator.enlargeReactionModel(ReactionModelGenerator.java:3858)
    at jing.rxnSys.ReactionModelGenerator.modelGeneration(ReactionModelGenerator.java:1457)
    at RMG.main(RMG.java:96)
Caused by: java.lang.ClassNotFoundException: jing.chem.molFile
    at java.net.URLClassLoader$1.run(URLClassLoader.java:214)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.net.URLClassLoader.findClass(URLClassLoader.java:205)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:321)
    at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:266)
    ... 15 more
Caused by: java.util.zip.ZipException: error reading zip file
    at java.util.zip.ZipFile.read(Native Method)
    at java.util.zip.ZipFile.access$1200(ZipFile.java:46)
    at java.util.zip.ZipFile$ZipFileInputStream.read(ZipFile.java:464)
    at java.util.zip.ZipFile$1.fill(ZipFile.java:247)
    at java.util.zip.InflaterInputStream.read(InflaterInputStream.java:158)
    at java.util.jar.Manifest$FastInputStream.fill(Manifest.java:439)
    at java.util.jar.Manifest$FastInputStream.readLine(Manifest.java:375)
    at java.util.jar.Manifest$FastInputStream.readLine(Manifest.java:407)
    at java.util.jar.Attributes.read(Attributes.java:376)
    at java.util.jar.Manifest.read(Manifest.java:199)
    at java.util.jar.Manifest.(Manifest.java:69)
    at java.util.jar.JarFile.getManifestFromReference(JarFile.java:182)
    at java.util.jar.JarFile.getManifest(JarFile.java:163)
    at sun.misc.URLClassPath$JarLoader$2.getManifest(URLClassPath.java:710)
    at java.net.URLClassLoader.defineClass(URLClassLoader.java:238)
    at java.net.URLClassLoader.access$000(URLClassLoader.java:73)
    at java.net.URLClassLoader$1.run(URLClassLoader.java:212)
    ... 20 more

At time of death:

The model core has 4382 reactions and 97 species. The model edge has 13421 reactions and 5654 species. The chem.inp file has 100 species (excluding inert gases). The chem.inp file has 4394 reactions (excluding duplicates). Running time: 358.550 min Memory used: 286.85 MB / 1629.22 MB (17.61%)

(this is with my glarborg seed at commit 69ace86e0) This java code was compiled by ant at: 2011-03-03T17:01:53 The git repository was on the branch: seedmech And at the commit with the hash: 773b29b619806784be37f3c45d0afdca6f7aff2f

rwest commented 13 years ago

It happened in another job running alongside, at around the same time. I have an idea about this... I think it may occur when I rebuild the jar file that the job is running from. Usually it doesn't seem to care, because all the classes it needs are in memory or something. This always dies in the same place.

rwest commented 12 years ago

I think this must be as described in previous comment - a problem of rebuilding a running jar file - so I'm closing the issue. Reopen it if it reoccurs.